GeneBe

rs3215202

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_000809.4(GABRA4):​c.87-13_87-10delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000864 in 1,157,262 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 8.6e-7 ( 0 hom. )

Consequence

GABRA4
NM_000809.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.263

Publications

0 publications found
Variant links:
Genes affected
GABRA4 (HGNC:4078): (gamma-aminobutyric acid type A receptor subunit alpha4) Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA-A receptors, which are ligand-gated chloride channels. Chloride conductance of these channels can be modulated by agents such as benzodiazepines that bind to the GABA-A receptor. At least 16 distinct subunits of GABA-A receptors have been identified. This gene encodes subunit alpha-4, which is involved in the etiology of autism and eventually increases autism risk through interaction with another subunit, gamma-aminobutyric acid receptor beta-1 (GABRB1). Alternatively spliced transcript variants encoding different isoforms have been found in this gene.[provided by RefSeq, Feb 2011]
GABRA4 Gene-Disease associations (from GenCC):
  • genetic developmental and epileptic encephalopathy
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics, Illumina

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000809.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GABRA4
NM_000809.4
MANE Select
c.87-13_87-10delTTTT
intron
N/ANP_000800.2
GABRA4
NM_001204266.2
c.30-13_30-10delTTTT
intron
N/ANP_001191195.1
GABRA4
NM_001204267.2
c.30-13_30-10delTTTT
intron
N/ANP_001191196.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GABRA4
ENST00000264318.4
TSL:1 MANE Select
c.87-13_87-10delTTTT
intron
N/AENSP00000264318.3
GABRA4
ENST00000502874.1
TSL:5
n.86+380_86+383delTTTT
intron
N/AENSP00000424386.1
GABRA4
ENST00000508560.5
TSL:3
n.19-13_19-10delTTTT
intron
N/AENSP00000425445.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
8.64e-7
AC:
1
AN:
1157262
Hom.:
0
AF XY:
0.00000171
AC XY:
1
AN XY:
585378
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
26596
American (AMR)
AF:
0.00
AC:
0
AN:
36862
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22628
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36012
South Asian (SAS)
AF:
0.00
AC:
0
AN:
74638
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
47164
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4810
European-Non Finnish (NFE)
AF:
0.00000116
AC:
1
AN:
859186
Other (OTH)
AF:
0.00
AC:
0
AN:
49366
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.26

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs3215202; hg19: chr4-46994972; API